'\" t
.TH samtools-bedcov 1 "17 March 2021" "samtools-1.12" "Bioinformatics tools"
.SH NAME
samtools bedcov \- reports coverage over regions in a supplied BED file
.\"
.\" Copyright (C) 2008-2011, 2013-2018, 2020 Genome Research Ltd.
.\" Portions copyright (C) 2010, 2011 Broad Institute.
.\"
.\" Author: Heng Li <lh3@sanger.ac.uk>
.\" Author: Joshua C. Randall <jcrandall@alum.mit.edu>
.\"
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.SH SYNOPSIS
.PP
samtools bedcov
.RI [ options ]
.IR region.bed " " in1.sam | in1.bam | in1.cram "[...]"

.SH DESCRIPTION
.PP

Reports the total read base count (i.e. the sum of per base read depths)
for each genomic region specified in the supplied BED file. The regions
are output as they appear in the BED file and are 0-based.
Counts for each alignment file supplied are reported in separate columns.

.SH OPTIONS
.TP
.BI "-Q " INT
.RI "Only count reads with mapping quality greater than " INT
.TP
.BI "-g " FLAGS
By default, reads that have any of the flags UNMAP, SECONDARY, QCFAIL,
or DUP set are skipped. To include these reads back in the analysis, use
this option together with the desired flag or flag combination.
.I FLAGS
can be specified in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/),
in octal by beginning with `0' (i.e. /^0[0-7]+/), as a decimal number
not beginning with '0' or as a comma-separated list of flag names. [0]

For a list of flag names see
.IR samtools-flags (1).
.TP
.BI "-G " FLAGS
Discard any read that has any of the flags specified by
.I FLAGS
set.  FLAGS are specified as for the
.B "-g"
option. [UNMAP,SECONDARY,QCFAIL,DUP]
.TP
.B  -j
Do not include deletions (D) and ref skips (N) in bedcov computation.
.TP
.BI "-d " INT
Print an additional column, for each file, containing the number of bases having
a depth above and including the given threshold. If the option is not used, the
extra column is not displayed. The option value must be an integer >= 0.
.TP
.B "-X"
If this option is set, it will allows user to specify customized index file location(s) if the data
folder does not contain any index file. Example usage: samtools bedcov [options] -X <in.bed> </data_folder/in1.bam> [...] </index_folder/index1.bai> [...]

.SH AUTHOR
.PP
Written by Heng Li from the Sanger Institute.

.SH SEE ALSO
.IR samtools (1)
.PP
Samtools website: <http://www.htslib.org/>
